[gmx-users] coupling issue

[Justin Lemkul]

On 5/16/13 8:12 AM, gromacs query wrote:
> Dear All,
>
> I have a system with two solutes (A and B) with water and ions. For
> pressure coupling in index file I defined two groups: Solute and Solvent,
> where solute consists of A+B and solvent consists of water+ions
>
> Due to some reasons I need to apply position restraints on Solute A only
> for few ns NPT run then make it free also. So while doing NPT run and using
> above said two groups in pressure coupling; that is Solute (A+B) and
> Solvent (water+ions) I get this Warning:
>
> You are using pressure coupling with absolute position restraints, this
> will give artifacts. Use the refcoord_scaling option.
>
>
> Should I ignore this warning or do any of following:
>
> 1) Defining two groups: One with Solute A only and Second group with
> SoluteB+Water+ions
>

The error arises due to pressure coupling, not temperature coupling.  I don't 
think you necessarily need to split up the temperature coupling groups differently.

> 2) I am not sure which option I should use for refcoord_scaling option
>

In almost all cases, use the 'com' setting for refcoord_scaling.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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